Functions
This section lists the functions implemented in SeqAn. Note that SeqAn uses global functions to access data types, e.g. the length of a string str is determined by calling length(str) and not by calling a member function str.length().
Functions
getScaleAccess function returning the distance dependent scaling factor used for PAM matrix computation
Alignments
assignSourceAssigns the source to a new value.
clearGapsRemove blanks from a gapped sequence.
colA column in an alignment.
colsThe container of columns in an alignment.
countGapsCount blanks at a specific position in a gapped sequence.
createSourceCreates a new source.
dependentSourceTest if object depends from it's source.
detachMakes an object independent from other objects.
emptySourceTest if there is a source.
gapValueReturns reference to a value that is used as gap character.
globalAlignmentComputes the best global alignment of the two sequences.
heaviestIncreasingSubsequenceComputes the heaviest increasing subsequence.
insertGapInsert one blank into a gapped sequence.
insertGapsInsert blanks into a gapped sequence.
isGapTest a gapped sequence for gaps at a specific position.
localAlignmentComputes the best local alignment of two sequences.
longestCommonSubsequenceComputes the longest common subsequence.
longestIncreasingSubsequenceComputes the longest increasing subsequence.
matchRefinementRefines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping.
moveSourceMoves the source to a new value.
multiLocalAlignmentComputes multiple local alignments of two sequences.
removeGapRemoves one blank from a gapped sequence.
removeGapsRemoves blanks from a gapped sequence.
rowA row in an alignment.
rowsThe container of rows in an alignment.
scoreGapScore for gaps.
scoreGapExtendScore for extending gaps.
scoreGapOpenScore for opening a gap.
scoreMatchMatch score.
scoreMismatchMismatch score.
setSourceLet an external object be the source.
setStringsLoads the sequences of a stringset into an alignment.
smithWatermanComputes the best local alignment of the (two) sequences given in align.
smithWatermanGetNextComputes next best local alignment.
sourceThe source of an object.
sourceBeginBegin of the source segment.
sourceEndEnd of the source segment.
sourceLengthLength of the source.
sourceSegmentThe used part of the source.
Alphabets
convertConverts a value into another value.
gapValueReturns reference to a value that is used as gap character.
infimumValueInfimum for a given type.
ordValueMaps an alphabet 1-to-1 to the interval [0..ValueSize).
supremumValueSupremum for a given type.
Array Handling
arrayClearSpaceDestroys the begin of an array and keeps the rest.
arrayConstructConstruct objects in a given memory buffer.
arrayConstructCopyCopy constructs an array of objects into in a given memory buffer.
arrayConstructMoveMove constructs an array of objects into in a given memory buffer.
arrayCopyCopies a range of objects into another range of objects.
arrayCopyBackwardCopies a range of objects into another range of objects starting from the last element.
arrayCopyForwardCopies a range of objects into another range of objects starting from the first element.
arrayDestructDestroys an array of objects.
arrayFillAssigns one object to each element of a range.
arrayMoveMoves a range of objects into another range of objects.
arrayMoveBackwardMoves a range of objects into another range of objects starting from the last element.
arrayMoveForwardMoves a range of objects into another range of objects starting from the first element.
Blast
atBeginDetermines whether an iterator is at the beginning position.
atBeginDetermines whether an iterator is at the beginning position.
atEndDetermines whether an iterator is at the end position.
atEndDetermines whether an iterator is at the end position.
atEndDetermines whether an iterator is at the end position.
databaseNameReference to the name (identifier) of the database in a Blast report.
databaseOrientationPlusOrientation of the database sequence within a Blast HSP alignment.
getAlignmentTurns a HSP from a Blast search into an Alignment object.
getAlignmentTurns a HSP from a Blast search into an Alignment object.
getBitScoreThe bit score associated with a Blast HSP.
getDatabaseBeginThe begin position of the HSP on the database sequence.
getDatabaseEndThe end position of the HSP on the database sequence.
getDatabaseNameThe name (identifier) of the database in a Blast report.
getEValueThe e-value associated with a Blast HSP.
getEValueCutoffThe Expect-Value cutoff parsed from a Blast report.
getGappedKappaThe gapped kappa value parsed from a Blast report.
getGappedLambdaThe lambda value parsed from a Blast report.
getGetExtensionThe gap extension penalty parsed from a Blast report.
getGetOpenThe gap open penalty parsed from a Blast report.
getKappaThe kappa value parsed from a Blast report.
getLambdaThe lambda value parsed from a Blast report.
getNextGet next Blast report from a file containing multiple Blast reports.
getNumGapsThe number of gaps within a Blast HSP alignment.
getQueryBeginThe begin position of the HSP on the query sequence.
getQueryEndThe end position of the HSP on the query sequence.
getQueryNameThe name (identifier) of the query in a Blast report.
getScoreThe Smith-Waterman score associated with a Blast HSP.
getValueAccess to the value.
getValueAccess to the value.
goBeginIterates to the first position of a container.
goBeginIterates to the first position of a container.
goEndIterates to the last position of a container.
goNextIterates to next position.
goNextIterates to next position.
goPreviousIterates to pevious position.
hostHitThe BlastHit this iterator is working on.
hostReportThe BlastReport this iterator is working on.
lengthThe number of items/characters.
numHitsThe total number of hits in a Blast report.
numHspsThe number of HSPs for an entire Blast report or for one Blast hit.
queryNameReference to the name (identifier) of the query in a Blast report.
queryOrientationPlusOrientation of the query sequence within a Blast HSP alignment.
readLoads records from a file.
valueReference to the value.
valueReference to the value.
Chaining
chainComputes the chain on a set of fragments.
Comparisons
compareCompares two objects.
hasPrefixTest whether a sequence is prefix of another sequence.
isEqualOperator "==".
isGreaterOperator ">".
isGreaterOrEqualOperator ">=".
isLessOperator "<".
isLessOrEqualOperator "<=".
isNotEqualOperator "!=".
isPrefixTest whether a sequence is prefix of another sequence.
lcpLengthLength of longest common prefix.
Containers
backThe last item in container.
beginThe begin of a container.
beginPositionBegin position of object in host.
capacityThe maximal length.
clearResets an object.
emptyTest a container for being empty.
endThe end of a container.
endPositionEnd position of object in host.
eraseErases a part of a container
fillResizes and fills a container.
frontThe first item in container.
getValueAccess to the value.
infixCreates infix object.
infixWithLengthCreates infix object.
iterIterator to item at given position.
lengthThe number of items/characters.
prefixCreates prefix object.
reserveIncreases the capacity.
resizeChanges the length.
resizeSpaceMakes free space in container
shrinkToFitResizes container to minimum capacity
suffixCreates suffix object.
toCStringAccess sequence as c-style string.
valueReference to the value.
Content Manipulation
appendConcatenate two containers.
appendValueAppends a value to a container.
assignAssigns one object to another object.
assignValueAssigns value to item.
getValueAccess to the value.
insertValueInserts a single value into a container.
moveHands over content from one container to another container.
moveValueAssigns value to item.
popDeletes item with the highest priority and adjusts the priority queue.
pushInserts a new item and adjusts the priority queue if necessary.
replaceReplaces a part of a container with another container.
setAssigns one object to another object avoiding to copy contents.
setValueMakes holder dependent.
topReference to the item with the highest priority.
valueConstructConstructs an object at specified position.
valueConstructMoveMove constructs an object at specified position.
valueDestructDestoys an object at specified position.
Dependent Objects
addRefCalled when dependency is added.
createMakes an object to owner of its content.
dependentTest whether object depends on other objects.
detachMakes an object independent from other objects.
hostThe object a given object depends on.
releaseRefCalled when dependency is released.
setBeginSets begin of object in host.
setBeginPositionSets begin position of object in host.
setEndSets end of object in host.
setEndPositionSets begin position of object in host.
setHostSets the host of an object.
Graph
addEdgeAdds a new edge to the graph, either with or without cargo.
addEdgesShortcut to add multiple edges at once. Creates vertices implicitly.
addVertexAdds a new vertex to the graph.
alignmentEvaluationGiven a multiple alignment, this function calculates all kinds of alignment statistics.
all_pairs_shortest_pathFinds shortest paths between all pairs of vertices in a graph.
assignCargoAssigns a new cargo to the edge.
assignNextSAssigns another EdgeStump to the next source pointer.
assignNextTAssigns another EdgeStump to the next target pointer.
assignPropertyAssigns a property to an item in the property map.
assignSourceAssigns a source vertex to an edge.
assignTargetAssigns a target vertex to an edge.
atBeginDetermines whether an iterator is at the beginning position.
atEndDetermines whether an iterator is at the end position.
bellman_ford_algorithmComputes shortest paths from a single source in a graph.
breadth_first_searchImplements a breadth-first search on a graph.
cargoAccess to the cargo.
clearResets an object.
clearEdgesRemoves all edges in a graph.
clearVerticesRemoves all vertices in a graph.
combineGraphsCombines multiple alignment graphs into one single graph.
connected_componentsDecomposes an undirected graph into its connected components.
dag_shortest_pathComputes shortest paths from a single source in a directed acyclic graph (DAG).
degreeNumber of incident edges for a given vertex.
depth_first_searchImplements a depth-first search on a graph.
dijkstraComputes shortest paths from a single source in a graph.
emptyTest a container for being empty.
findEdgeFinds an edge.
floyd_warshallFinds shortest paths between all pairs of vertices in a graph.
ford_fulkersonComputes a maximum flow in a directed graph.
getAdjacencyMatrixReturns an adjacency matrix representation of the graph.
getCargoGet method for the edge cargo.
getDistanceMatrixComputes a pairwise distance matrix from an alignment graph.
getIdLowerBoundReturns the smallest distributed id. That is, the return value is guaranteed to be the smallest id obtained so far.
getIdUpperBoundReturns the largest distributed id plus 1. That is, the return value is guaranteed to be an upper bound on all distributed ids.
getNextSGet method for the next source pointer.
getNextTGet method for the next target pointer.
getNilUtility function returning a value that represents nil. Useful for various graph algorithms, e.g., missing predecessors, vertices that have not been visited, etc.
getPropertyGet method for an item's property.
getSourceGet method for the source.
getTargetGet method for the target.
getValueAccess to the value.
goBeginIterates to the first position of a container.
goEndIterates to the last position of a container.
goNextIterates to next position.
goPreviousIterates to pevious position.
hostGraphThe graph this iterator is working on.
idCountDetermines the number of ids that were obtained.
idInUseChecks whether the given id is in use or not.
inDegreeNumber of incoming edges for a given vertex.
kruskals_algorithmComputes a minimum spanning tree on a graph.
nextSAccesses the next source pointer.
nextTAccesses the next target pointer.
numEdgesNumber of edges in a graph.
numVerticesNumber of vertices in a graph.
obtainIdObtains a new id from the id manager.
outDegreeNumber of outgoing edges for a given vertex.
prims_algorithmComputes a minimum spanning tree on a graph.
progressiveAlignmentPerforms a progressive alignment.
propertyAccesses the property of an item in the property map.
releaseAllReleases all ids handled by this id manager at once.
releaseIdReleases a given id so it can be redistributed later on.
removeEdgeRemoves an edge from the graph. For automatons a label is required.
removeInEdgesRemoves the incoming edges of a given vertex.
removeOutEdgesRemoves the outgoing edges of a given vertex.
removeVertexRemoves a vertex.
resizeEdgeMapInitializes an edge map
resizeVertexMapInitializes a vertex map.
slowNjTreeComputes a guide tree from a distance matrix.
sourceVertexReturns the source vertex of an edge.
strongly_connected_componentsDecomposes a directed graph into its strongly connected components.
sumOfPairsScoreGiven a multiple alignment, this function calculates the sum-of-pairs score.
targetAccesses the target of an EdgeStump.
targetVertexReturns the target vertex of an edge.
topological_sortPerforms a topological sort on a directed acyclic graph (DAG).
transitive_closureDetermines whether there is a path between any two given vertices or not.
transposeTransposes a graph, either in-place or from source to dest.
tripletLibraryExtensionPerforms the consistency extension proposed in T-Coffee.
upgmaTreeComputes a guide tree from a distance matrix.
valueReference to the value.
Graph: Alignment Graph
assignStringSetAssigns a new string set to an alignment graph.
convertAlignmentConverts an alignment graph into an alignment matrix.
findVertexFinds a vertex given a sequence id and a position.
fragmentBeginGets the begin position for this vertex descriptor in the sequence.
fragmentLengthGets the length of the label of a given vertex descriptor in the sequence.
getFirstCoveredPositionFinds the first position in a sequence that is not assigned to a nil vertex.
getLastCoveredPositionFinds the last position in a sequence that is not assigned to a nil vertex.
getStringSetGets the string set of an alignment graph.
labelGets the label that is associated with this vertex descriptor.
sequenceIdGets the sequence id that is associated with this vertex descriptor.
stringSetGets the string set of an alignment graph.
Graph: Automaton
assignRootAssigns a new root vertex to the automaton.
createRootCreates the root in a tree or an automaton.
getRootGet method for the root of a tree or an automaton.
getSuccessorGets the successor for a given vertex and an edge label. For an automaton a single character is required whereas for a word graph getSuccessor takes a string.
isRootTests whether a given vertex is the root or not.
labelReturns the label of the out-edge this iterator points to.
parseStringParses a string one character at a time and moves accordingly in the automaton.
rootGets a reference to the root of the tree.
Graph: Hmm
assignBeginStateAssigns a begin state.
assignEmissionProbabilityAssigns a new emission probability.
assignEndStateAssigns an end state.
assignTransitionProbabilityAssigns a new transition probability.
backwardAlgorithmImplements the backward algorithm.
beginStateReturns a reference to the begin state.
emissionProbabilityReturns a reference to the emission probability.
endStateReturns a reference to the end state.
forwardAlgorithmImplements the forward algorithm.
getBeginStateReturns the begin state.
getEmissionProbabilityReturns the emission probability.
getEndStateReturns the end state.
getTransitionProbabilityReturns the transition probability.
transitionProbabilityReturns a reference to the transition probability.
viterbiAlgorithmImplements the viterbi algorithm.
Graph: Oracle
createOracleCreates a factor oracle.
createOracleOnReverseCreates a factor oracle for the reversed string.
Graph: Tree
addChildAdds a new child vertex to a parent vertex. Optionally a cargo can be attached to the parent-child edge.
assignRootAssigns a new root vertex to the automaton.
childVertexReturns the child vertex of an edge.
collectLeavesReturns all leaves underneath a given vertex.
createRootCreates the root in a tree or an automaton.
getRootGet method for the root of a tree or an automaton.
isLeafTests whether a given vertex is a leaf or not.
isRootTests whether a given vertex is the root or not.
numChildrenNumber of children of a given tree vertex.
numTreeEdgesNumber of tree edges.
parentVertexReturns the parent vertex of an edge.
removeAllChildrenRemoves all children from the tree given a parent.
removeChildRemoves a child from the tree given a parent.
rootGets a reference to the root of the tree.
Graph: Trie
createTrieCreates a trie.
createTrieOnReverseCreates a trie for all reversed keywords.
Graph: Word Graph
getSuccessorGets the successor for a given vertex and an edge label. For an automaton a single character is required whereas for a word graph getSuccessor takes a string.
parseStringParses a string one character at a time and moves accordingly in the automaton.
Index
alignmentReturns an alignment of the occurences of the representative substring in the index text.
bwtAtShortcut for value(indexBWT(..), ..).
childAtShortcut for value(indexChildTab(..), ..).
childrenAreLeavesTest whether iterator points to a node with only leaf-children.
countChildrenCount the number of children of a tree node.
countOccurrencesReturns the number of occurences of representative in the index text.
createBWTableCreates a Burrows-Wheeler table from a given text and suffix array.
createChildTableCreates a child table from a given lcp table.
createCountArrayBuilds an index on a StringSet storing how often a q-gram occurs in each sequence.
createLCPTableCreates a lcp table from a given text and suffix array.
createQGramIndexBuilds a q-gram index on a sequence.
createQGramIndexDirOnlyBuilds the directory of a q-gram index on a sequence.
createQGramIndexSAOnlyBuilds the suffix array of a q-gram index on a sequence.
createSuffixArrayCreates a suffix array from a given text.
createWotdIndexBuilds a q-gram index on a sequence.
dirAtShortcut for value(indexDir(..), ..).
emptyParentEdgeReturns true iff the edge label from the iterator node to its parent is empty.
getFibreReturns a specific Fibre of an Index object.
getFrequencyReturns the number of sequences, which contain the representative as a substring.
getOccurrenceReturns an occurence of the representative substring in the index text.
getOccurrencesReturns all occurences of the representative substring in the index text.
getOccurrencesBWTReturns the characters left beside all occurence of the representative substring in the index text.
goDownIterates down one edge or a path in a tree.
goRightIterates to the next sibling in a tree.
goUpIterates up one edge to the parent in a tree.
hashComputes a (lower) hash value for a shape applied to a sequence.
hash2Computes a unique hash value of a shape, even if it is shorter than its span.
hash2NextComputes a unique hash value for the adjacent shape, even if it is shorter than q.
hashNextComputes the hash value for the adjacent shape.
hashUpperComputes an upper hash value for a shape applied to a sequence.
indexBWTShortcut for getFibre(.., ESA_BWT).
indexChildTabShortcut for getFibre(.., ESA_ChildTab).
indexCreateCreates a specific Fibre.
indexDirShortcut for getFibre(.., QGram_Dir).
indexLCPShortcut for getFibre(.., ESA_LCP).
indexLCPEShortcut for getFibre(.., ESA_LCPE).
indexRawSAShortcut for getFibre(.., ESA_RawSA).
indexRawTextShortcut for getFibre(.., ESA_RawText).
indexRequireOn-demand creation of a specific Fibre.
indexSAShortcut for getFibre(.., ESA_SA).
indexShapeShortcut for getFibre(.., QGram_Shape).
indexSuppliedReturns whether a specific Fibre is present.
indexTextShortcut for getFibre(.., ESA_Text).
isLeafTest whether iterator points to a leaf.
isLeftMaximalTest whether the occurences of an iterator's representative mutually differ in the character left of the hits.
isPartiallyLeftExtensibleTest whether the characters left of the two occurences of representative are equal.
isRightTerminalTest whether iterator points to a suffix.
isRootTest whether iterator points to the root node.
isUniqueTest whether the representative occurs only once in every sequence.
lcaReturns the last common ancestor of two tree nodes.
lcpReturns the length of the longest-common-prefix of two Suffix Tree nodes.
lcpAtShortcut for value(indexLCP(..), ..).
lcpeAtShortcut for value(indexLCPE(..), ..).
nodeHullPredicateIf false this node and its subtree is concealed.
nodePredicateIf false this node will be skipped during the bottom-up traversal.
orderOccurrencesSorts a string of occurrences.
parentEdgeFirstCharReturns the first character of the edge from an iterator node to its parent.
parentEdgeLabelReturns a substring representing the edge from an iterator node to its parent.
parentEdgeLengthReturns the length of the edge from the iterator node to its parent.
parentRepLengthReturns the length of the substring representing the path from root to iterator's parent node.
rawtextAtShortcut for value(indexRawText(..), ..).
repLengthReturns the length of the substring representing the path from root to iterator node.
representativeReturns a substring representing the path from root to iterator node.
saAtShortcut for value(indexSA(..), ..).
stringToShapeTakes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object.
weightNumber of relevant positions in a shape.
Input/Output
areadAtAsynchronously loads records from a specific position in a file.
awriteAtAsynchronously saves records to a specific position in a file.
cancelCancels an asynchronous request.
closeCloses a file.
flushWaits for all open requests to complete.
goNextIterates to next position.
guessFileFormatTries to determine the format of a file.
lengthThe number of items/characters.
openOpens a file.
openTempOpens a temporary file.
readLoads a record from file.
readLoads records from a file.
readAtLoads records from a specific position in a file.
readFeatureFinds the first feature specified by 'key' starting from position 'start' in the feature table (the feature table can be obtained by calling readLineType with the two-character code "FT").
readLineTypeReads the information belonging to the two-character line code specified.
readMetaRead meta information from file.
resizeChanges the length.
rewindSets the current file pointer to the beginning.
seekChanges the current file pointer.
setEOFSets the file end to the current pointer.
sizeGets the file size.
tellGets the current file pointer.
waitForWaits for an asynchronous request to complete.
writeWrites to stream.
writeSaves records to a file.
writeAtSaves records to a specific position in a file.
Iteration
assignValueAssigns value to item.
atBeginDetermines whether an iterator is at the beginning position.
atEndDetermines whether an iterator is at the end position.
atNilTests whether iterator is at nil position.
beginThe begin of a container.
containerContainer of an iterator.
differenceThe difference between two iterators.
endThe end of a container.
getValueAccess to the value.
goBeginIterates to the first position of a container.
goEndIterates to the last position of a container.
goFurtherIterates some steps further.
goNextIterates to next position.
goNilMoves iterator to nil position.
goPreviousIterates to pevious position.
moveValueAssigns value to item.
positionPosition of an iterator.
valueReference to the value.
Map
addInsert another value into a multi map.
cargoReturns a cargo given a key.
eraseRemoves a value from a map.
eraseAllRemoves a value from a map.
findFind a value in a map.
hasKeyDetermines whether a map contains a value given key.
insertInsert new value into map.
mapValueSubscript operator [ ] of maps.
valueReturns a value given a key.
Memory
allocateAllocates memory from heap.
clearDeallocates all memory blocks.
deallocateDeallocates memory.
Miscellaneous
addOptionadds an instance of CommandLineOption to the CommandLineParser
adjustTopAdjusts the priority of the first item.
appendCmdLineadds a line of text to the help output of the CommandLineParser
argumentCountReturns the count of passed arguments.
getArgumentValueFills the passed variable value with the argument set on the command line.
getOptionValueFills the passed variable value with the value set for the option on the command line.
hasOptionReturns true if the there is an option registered in the parser, that has the passed optionIdentifier
helpPrints the complete help message for your parser to the stream.
helpTextReturns the help text associated with the CommandLineOption object
idA value that identifies the underlying sequence.
isSetReturns true if the option was set on the parsed command line.
log2Computes logarithm of base 2 for integer types
longNameReturns the long option name of a CommandLineOption object
parseReturns true if the option was set on the parsed command line.
requiredArgumentsusing this option you can define how many non parameterized options are required by your program.
setHelpTextSets the help text associated with the CommandLineOption object
setLongNameSets the long option name of a CommandLineOption object
setShortNameSets the short option name of a CommandLineOption object
shareResourcesDetermines whether two sequences share the same resource.
shortHelpPrints a short help message for your parser to the stream
shortNameReturns the short option name of a CommandLineOption object
Motif Search
absFreqOfLettersInSeqCounts the number of times each residue of a fixed sequence alphabet occurs in a given sequence.
absFreqOfLettersInSetOfSeqsCounts the number of times each residue of a fixed sequence alphabet occurs in a given set of sequences.
addValueAdds a value of a specific type to each element of a given FrequencyDistribution object.
backgroundFrequencyDetermines the background letter frequencies in a given dataset
binomialCoefficientCalculates the binomial coefficient C(n,k).
completeProfileConcatenates the background frequency with the profile for the motif component.
convertPatternToProfileConverts a pattern into a profile which consists of a set of frequency distributions.
convertResidueToFrequencyDistCoverts a residue to a frequency distribution (profile).
convertSetOfPatternsToProfileConverts a set of sequence patterns into a profile.
determineConsensusSeqDetermines the consensus pattern of a given profile.
displayDisplays a given set of strings.
displayResultDisplays all found motif candidates. In the case of the Projection Motif Finder the function displays the consensus pattern of the found motif candidate.
emRepresents the EM algorithm as used by MEME.
factorialCalculates the factorial value of any integer number.
findMotifRepresents the main function which is used to start the search for noticeable motif patterns.
hammingDistanceDetermines the Hamming distance between two sequences.
inverseHashDetermines the corresponding sequence pattern given the hash value.
logarithmizeLogarithmizes each element of a given FrequencyDistribution object.
normalizeDetermines the normalized frequencies.
posOfMaxDetermines the residue position in a given FrequencyDistribution object with the maximum frequency.
sumDetermines the sum of all frequencies in a given FrequencyDistribution object.
Pipelining
beginReadInitiates a read process.
beginWriteInitiates a write process.
bundle2Returns a bundle of two objects.
bundle3Returns a bundle of three objects.
bundle5Returns a bundle of five objects.
endReadTerminates a read process.
endWriteTerminates a write process.
frontGets the first element of the remaining stream.
popPops the first element of the remaining stream.
pushAppends an item at the end of an input stream.
Scoring
buildPamCoordinates computation by invokating extrapolation, alphabet extension, rounding, scaling, type conversion and symmetrization.
getDistreturns the distance on which PAM matrix computation is based.
getEntropyreturns entropy of the PAM matrix.
scoreThe score for aligning two values according to a scoring scheme.
Searching
findSearch for a Pattern in a Finder object.
getScoreScore of the last found match in approximate searching.
haystackReturns the haystack of a Finder object.
needleReturns the needle of a Pattern object (not implemented for some online-algorithms).
scoreLimitThe minimal score a match must reach in approximate searching.
scoringSchemeThe scoring scheme used for finding or aligning.
setHaystackSets the haystack of a Finder object.
setNeedleSets the needle of a Pattern object and optionally induces preprocessing.
setPositionSets the position of a finder.
setScoreLimitSets the minimal score a match must reach in approximate searching.
setScoringSchemeSets the scoring scheme used for finding or aligning.
Seed Handling
addSeedAdds a seed to an existing set.
addSeedsAdds several seeds to an existing set. If a merging or chaining algorithm is used seeds are added if the merging or chaining fails.
appendDiag Adds diagonal to the seed.
bandedAlignmentCalculates a banded alignment around a Seed.
bandedChainAlignment Calculates a banded alignment around a chain of seeds.
endDiagonal Returns the diagonal of the end point.
extendSeed Extends a seed.
extendSeeds Extenstion of seeds.
getAlignment Constructs a alignment from a MultiSeed.
globalChaining Calculates the best global chain using the Gusfield-Algorithm with scores (ManhattanDistance) and without.
leftDiagonal Returns the most left diagonal of the seed (maximum diagonal value).
leftDim0 Returns the first position of the seed in the query.
leftDim1 Returns the first position of the seed in the database.
maximumDistanceSets the maximal distance between two seed during a chaining process.
obtainID btains a new id from the id manager.
qualityValueSets the minimum length for a seed to be saved permanently.
releaseID Releases a given id so it can be redistributed later on.
rightDiagonal Returns the most right diagonal of the seed (minimum diagonal value).
rightDim0 Returns the last position of the seed in the query.
rightDim1 Returns the last position of the seed in the database.
scoreSeed Calculates the score of a seed.
seedScoreReturns the score of a seed.
setLeftDiagonal Sets a new value for the most left diagonal.
setLeftDim0 Updates the start point of the seed.
setLeftDim1 Updates the start point of the seed.
setMaximumDistanceSets the maximal distance between two seed during a chaining process.
setQualityValueSets the minimum length for a seed to be saved permanently.
setRightDiagonal Sets a new value for the most right diagonal.
setRightDim0 Updates the end point of the seed.
setRightDim1 Updates the end point of the seed.
startDiagonal Returns the diagonal of the start point.
Sequences
assignValueByIdAdds a new string to the StringSet and returns an id.
getSeqNoReturns the sequence number of a position.
getSeqOffsetReturns the local sequence offset of a position.
getValueByIdRetrieves a string from the StringSet given an id.
idToPositionRetrieves the position of a string in the StringSet given an id.
posGlobalizeConverts a local/global to a global position.
posLocalizeConverts a local/global to a local position.
positionToIdRetrieves the id of a string in the StringSet given a position.
removeValueByIdRemoves a string from the StringSet given an id.
stringSetLimitsRetrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions.
subsetCreates a subset of a given StringSet.
valueByIdRetrieves a string from the StringSet given an id.
SeqAn - Sequence Analysis Library - www.seqan.de